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- PDB-1hfk: Asparaginase from Erwinia chrysanthemi, hexagonal form with weak ... -

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Basic information

Entry
Database: PDB / ID: 1hfk
TitleAsparaginase from Erwinia chrysanthemi, hexagonal form with weak sulfate
ComponentsL-ASPARAGINE AMIDOHYDROLASEAsparaginase
KeywordsHYDROLASE
Function / homology
Function and homology information


asparagine metabolic process / asparaginase / asparaginase activity
Similarity search - Function
L-asparaginase, N-terminal domain / Rossmann fold - #40 / L-asparaginase, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. ...L-asparaginase, N-terminal domain / Rossmann fold - #40 / L-asparaginase, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. / Asparaginase / Asparaginase/glutaminase-like / L-asparaginase, N-terminal / Asparaginase/glutaminase-like superfamily / L-asparaginase, N-terminal domain superfamily / Asparaginase, N-terminal / Asparaginase / glutaminase domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesERWINIA CHRYSANTHEMI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsLubkowski, J. / Palm, G.J. / Kozak, M. / Jaskolski, M. / Wlodawer, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structures of Two Highly Homologous Bacterial L-Asparaginases: A Case of Enantiomorphic Space Groups
Authors: Jaskolski, M. / Kozak, M. / Lubkowski, J. / Palm, G.J. / Wlodawer, A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal Structure of Escherichia Coli L-Asparaginase, an Enzyme Used in Cancer Therapy
Authors: Swain, A.L. / Jaskolski, M. / Housset, D. / Rao, J.K.M. / Wlodawer, A.
#2: Journal: FEBS Lett. / Year: 1993
Title: A Left-Handed Crossover Involved in Amidohydrolase Catalysis, Crystal Structure of Erwinia Chrysanthemi L-Asparaginase with Bound L-Aspartate
Authors: Miller, M. / Rao, J.K.M. / Wlodawer, A. / Gribskov, M.R.
History
DepositionDec 5, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-ASPARAGINE AMIDOHYDROLASE
C: L-ASPARAGINE AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4384
Polymers70,2462
Non-polymers1922
Water7,620423
1
A: L-ASPARAGINE AMIDOHYDROLASE
C: L-ASPARAGINE AMIDOHYDROLASE
hetero molecules

A: L-ASPARAGINE AMIDOHYDROLASE
C: L-ASPARAGINE AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,8768
Polymers140,4924
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area16590 Å2
ΔGint-101.5 kcal/mol
Surface area38170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.720, 90.720, 339.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.989565, -0.016041, -0.143189), (-0.019021, -0.970542, 0.24018), (-0.142824, 0.240398, 0.96011)
Vector: -3.56105, 91.48508, -11.4709)
DetailsBIOLOGICAL_UNIT: HOMOTETRAMERIN THE TETRAMER TWO ACTIVE SITES ARE FORMED BY EACH INTIMATE DIMER AC AND ITS CRYSTALLOGRAPHIC SYMMETRY MATE

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Components

#1: Protein L-ASPARAGINE AMIDOHYDROLASE / Asparaginase / L-ASPARAGINASE / L-ASNASE


Mass: 35123.020 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THE NEW NAME OF ERWINIA CHRYSANTHEMI IS PECTOBACTERIUM CHRYSANTHEMI.
Source: (natural) ERWINIA CHRYSANTHEMI (bacteria) / Strain: NCPPB 1125 / References: UniProt: P06608, asparaginase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1 TO 21 IN THE DATABASE ENTRY CONSTITUTE THE LEADER PEPTIDE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 56 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: HANGING DROP. PROTEIN SOLUTION: 35 MG/ML PROTEIN, 0.1 M CHES PH 8.5. WELL SOLUTION: 47% AMMONIUM SULFATE, 2% PEG 400. CRYSTALS CROSSLINKED WITH 0.05% GLUTARALDEHYDE. SOAKED IN 40% PEG 6000, ...Details: HANGING DROP. PROTEIN SOLUTION: 35 MG/ML PROTEIN, 0.1 M CHES PH 8.5. WELL SOLUTION: 47% AMMONIUM SULFATE, 2% PEG 400. CRYSTALS CROSSLINKED WITH 0.05% GLUTARALDEHYDE. SOAKED IN 40% PEG 6000, 100 MM NAOAC, 100 MM 4-HYDROXY- LYSINE, PH 5.5.
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4.8 / Method: vapor diffusion / Details: Kozak, M., (2000) Acta Biochim. Pol., 47, 807.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
210 mMsodium citrate1drop
346-48 %MPD1reservoir
4100 mMsodium citrate1reservoir
510-20 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.928
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1995
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 2.17→20 Å / Num. obs: 29191 / % possible obs: 86.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 15.9 Å2 / Rsym value: 0.118 / Net I/σ(I): 7.1
Reflection shellResolution: 2.17→2.25 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.373 / % possible all: 71
Reflection
*PLUS
Num. measured all: 128226 / Rmerge(I) obs: 0.118
Reflection shell
*PLUS
% possible obs: 71 % / Rmerge(I) obs: 0.373

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1phasing
X-PLOR3.1phasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HFJ

1hfj


Resolution: 2.17→10 Å / Rfactor Rfree error: 0.0076 / Data cutoff high absF: 100000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: MLF (MAXIMUM LIKELYHOOD ON F'S)
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1101 2.5 %RANDOM
Rwork0.199 ---
obs0.199 36655 82.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.1 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso mean: 22.03 Å2
Baniso -1Baniso -2Baniso -3
1--3.511 Å21.806 Å20 Å2
2---3.511 Å20 Å2
3---7.021 Å2
Refine analyzeLuzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.17→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4706 0 10 423 5139
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.57
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.732
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.582.5
LS refinement shellResolution: 2.17→2.2 Å / Total num. of bins used: 22 /
RfactorNum. reflection
Rfree0.35 -
Rwork0.34 1312
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

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